We propose a biochemically plausible mechanism for constructing digital logic signals and gates of significant complexity within living cells. These mechanisms rely largely on co-opting existing biochemical machinery and ...

Amorphous computing is the development of organizational principles and programming languages for obtaining coherent behaviors from the cooperation of myriads of unreliable parts that are interconnected in unknown, ...

One of the hallmarks of biochemical circuits found in nature is analog, asymmetric, asynchronous design. That
is, there is little standardization of parts, e.g. all the promoters have different strengths and kinetics,
...

In this thesis, I present an engineering discipline for obtaining complex, predictable, and reliable cell behaviors by embedding biochemical logic circuits and programmed intercellular communications into cells. To accomplish ...

This distribution consists of 300 ng aliquots of plasmid DNA for each of twelve components and compound constructs utilizing our idempotent assembly strategy. The dried DNA should be stable at room temperature for many ...

The lack of standardization in assembly techniques for DNA sequences forces each DNA assembly
reaction to be both an experimental tool for addressing the current research topic, and an experiment
in and of itself. One ...

To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a ...

Why do biological risks exist? Can we develop and implement a strategy for thoughtfully approaching future biological risks? This short, working report provides an abstract introduction to the problem of biological risk ...

To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a ...

The next generations of both biological engineering and computer engineering demand that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems may provide us ...

Construction of complex biological systems can require assembling many
modules together. However, existing assembly schemes are lacking in
generality, ease of use, or power to perform some desirable
operations. Currently, ...

Natural biological systems are selected by evolution to continue to exist. Evolution might
give rise to complicated systems that are difficult to discover, measure, model, and direct.
Here, we redesign the genome of a ...

The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help ...

To date, engineered biological systems have been constructed via a variety of ad
hoc approaches. The resulting systems should be thought of as pieces of art. Here, I
propose to explore how existing forward engineering ...

This document provides background material in support of the 2005 intercollegiate Genetically Engineered Machine Competition (aka iGEM). Herein, you can read quick summaries of earlier competitions and courses, obtain a ...

The goal of Synthetic Biology is to engineer systems from biological parts. One class of systems are those whose purpose is to process information. My work seeks to build transcription-based devices for use in combinational ...

To date, engineered biological systems have been constructed via a variety of
ad hoc approaches. The resulting systems should be thought of as pieces of
art. We are interested in exploring how existing forward ...

The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help ...

The use of traditional tools for the discovery and characterization of biological systems has resulted in a wealth of biological knowledge. Unfortunately, only a small portion of the biological world is well-understood ...